Towards a method for rigorous development of generic requirements patterns

We present work in progress on a method for the engineering, validation and verification of generic requirements using domain engineering and formal methods. The need to develop a generic requirement set for subsequent system instantiation is complicated by the addition of the high levels of verification demanded by safety-critical domains such as avionics. Our chosen application domain is the failure detection and management function for engine control systems: here generic requirements drive a software product line of target systems. A pilot formal specification and design exercise is undertaken on a small (twosensor) system element. This exercise has a number of aims: to support the domain analysis, to gain a view of appropriate design abstractions, for a B novice to gain experience in the B method and tools, and to evaluate the usability and utility of that method.We also present a prototype method for the production and verification of a generic requirement set in our UML-based formal notation, UML-B, and tooling developed in support. The formal verification both of the structural generic requirement set, and of a particular application, is achieved via translation to the formal specification language, B, using our U2B and ProB tools

Preparation and Characterization of Covalently Binding of Rat Anti-human IgG Monolayer on Thiol-Modified Gold Surface

The 16-mercaptohexadecanoic acid (MHA) film and rat anti-human IgG protein monolayer were fabricated on gold substrates using self-assembled monolayer (SAM) method. The surface properties of the bare gold substrate, the MHA film and the protein monolayer were characterized by contact angle measurements, atomic force microscopy (AFM), grazing incidence X-ray diffraction (GIXRD) method and X-ray photoelectron spectroscopy, respectively. The contact angles of the MHA film and the protein monolayer were 18° and 12°, respectively, all being hydrophilic. AFM images show dissimilar topographic nanostructures between different surfaces, and the thickness of the MHA film and the protein monolayer was estimated to be 1.51 and 5.53 nm, respectively. The GIXRD 2θ degrees of the MHA film and the protein monolayer ranged from 0° to 15°, significantly smaller than that of the bare gold surface, but the MHA film and the protein monolayer displayed very different profiles and distributions of their diffraction peaks. Moreover, the spectra of binding energy measured from these different surfaces could be well fitted with either Au4f, S2p or N1s, respectively. Taken together, these results indicate that MHA film and protein monolayer were successfully formed with homogeneous surfaces, and thus demonstrate that the SAM method is a reliable technique for fabricating protein monolayer

High on-off conductance switching ratio in optically-driven self-assembled conjugated molecular systems

A new azobenzene-thiophene molecular switch is designed, synthesized and used to form self-assembled monolayers (SAM) on gold. An "on/off" conductance ratio up to 7x1E3 (with an average value of 1.5x1E3) is reported. The "on" conductance state is clearly identified to the cis isomer of the azobenzene moiety. The high "on/off" ratio is explained in terms of photo-induced, configuration-related, changes in the electrode-molecule interface energetics (changes in the energy position of the molecular orbitals with respect to the Fermi energy of electrodes) in addition to changes in the tunnel barrier length (length of the molecules). First principles DFT calculations demonstrate a better delocalization of the frontier orbitals, as well as a stronger electronic coupling between the azobenzene moiety and the electrode for the cis configuration over the trans one. Measured photoionization cross-sections for the molecules in the SAM are close to the known values for azobenzene derivatives in solution.Comment: 1 file with main text, figure and suppementary informatio

Strategies for Controlled Placement of Nanoscale Building Blocks

The capability of placing individual nanoscale building blocks on exact substrate locations in a controlled manner is one of the key requirements to realize future electronic, optical, and magnetic devices and sensors that are composed of such blocks. This article reviews some important advances in the strategies for controlled placement of nanoscale building blocks. In particular, we will overview template assisted placement that utilizes physical, molecular, or electrostatic templates, DNA-programmed assembly, placement using dielectrophoresis, approaches for non-close-packed assembly of spherical particles, and recent development of focused placement schemes including electrostatic funneling, focused placement via molecular gradient patterns, electrodynamic focusing of charged aerosols, and others

Molecular conformation in oligo(ethylene glycol) terminated self-assembled monolayers on gold and silver surfaces determines their ability to resist protein adsorption

We report data from infrared absorption (FTIR) and X-ray photoelectron spectroscopies that correlate the molecular conformation of oligo(ethylene glycol) (OEG)-terminated self-assembled alkanethiolate monolayers (SAMs) with the ability of these films to resist protein adsorption. We studied three different SAMs of alkanethiolates on both evaporated Au and Ag surfaces. The SAMs were formed from substituted 1-undecanethiols with either a hydroxyl-terminated hexa(ethylene glycol) (EG6-OH) or a methoxy-terminated tri(ethylene glycol) (EG3-OMe) end group, or a substituted 1-tridecanethiol chain with a methoxy-terminated tri(ethylene glycol) end group and a −CH2OCH3 side chain at the C-12 atom (EG[3,1]-OMe). The infrared data of EG6-OH-terminated SAMs on both Au and Ag surfaces reveal the presence of a crystalline helical OEG phase, coexisting with amorphous OEG moieties; the EG[3,1]-OMe-terminated alkanethiolates on Au and Ag show a lower absolute coverage and greater disorder than the two other compounds. The molecular conformation of the methoxy-terminated tri(ethylene glycol) (EG3-OMe) is different on Au and Ag surfaces due to the different lateral densities of SAMs on these substrates:  on Au we find a conformation similar to that of EG6-OH alkanethiolates, whereas on Ag the infrared spectra indicate a densely packed film with trans conformation around the C−C bonds of the glycol units. The resistance of these OEG-functionalized alkanethiolate SAMs to adsorption of fibrinogen from a buffered solution correlates with the molecular conformation of the OEG moieties. The predominantly crystalline helical and the amorphous forms of OEG on gold substrates are resistant to adsorption of proteins, while a densely packed “all-trans” form of EG3-OMe present on silver surfaces adsorbs protein. The experimental observations are compatible with the hypothesis that binding of interfacial water by the OEG moieties is important in their ability to resist protein adsorption